Pablo Andrés Gutiérrez

Detection of a complex of viruses in tamarillo (Solanum betaceum) orchards in the Andean region of Colombia

Tamarillo is one of the main fruit crops in the Andean region of Colombia. However, due to expansion of viral diseases, the cultivated area has undergone a rapid decline during recent years. In this work, we report the taxonomical identity of some of the viruses present in the main tamarillo producing regions in Colombia. The presence of AMV, CMV, PLRV, Potyvirus, ToMV, ToRSV and TSWV was evaluated by ELISA in the provinces of Antioquia, Boyaca, Cundinamarca, Narino and Putumayo. These results were complemented with RT-PCR and cDNA sequencing of the corresponding coat regions. Potyvirus, CMV and PLRV are the most predominant viruses, each virus being detected in at least one sample. Sequencing results revealed high levels of identity of PVY and PLRV from tamarillo with virus strains from potato crops, suggesting the possibility of cross infection. Our findings confirm that a virus complex is responsible for the decline of tamarillo productivity in Colombia.

Mitochondrial genome sequence of the potato powdery scab pathogen Spongospora subterranea

Abstract Spongospora subterranea is a soil-borne obligate parasite responsible for potato powdery scab disease. S. subterranea is a member of the order Plasmodiophorida, a protist taxa that is related to Cercozoa and Foraminifera but the fine details of these relationships remain unresolved. Currently there is only one available complete mtDNA sequence of a cercozoan, Bigelowiella natans. In this work, the mitochondrial sequence of a S. subterranea isolate infecting an Andean variety of S. tuberosum ssp. andigena (Diacol-Capiro) is presented. The mtDNA codes for 16 proteins of the respiratory chain, 11 ribosomal proteins, 3 ribosomal RNAs, 24 tRNAs, a RNA processing RNaseP, a RNA-directed polymerase, and two proteins of unknown function. This is the first report of a mtDNA genome sequence from a plasmodiophorid and will be useful in clarifying the phylogenetic relationship of this group to other members in the supergroup Rhizaria once more mtDNA sequences are available.

Genome sequence of a virus isolate from tamarillo (Solanum betaceum) in Colombia: evidence for a new potyvirus

Based on the results of a deep sequencing transcriptome study of tamarillo (Solanum betaceum), we report the genome sequence of a virus from this host plant. Since this probably represents a new member of the genus Potyvirus, the name tamarillo leaf malformation virus (TaLMV) has been proposed. Phylogenetic analysis reveals that TaLMV is the closest relative of Colombian datura virus (CDV), followed by three other potyviruses: tobacco etch virus, potato virus A and tobacco vein mottling virus. This is the first sequence of a potyvirus infecting Solanum betaceum containing the complete polyprotein coding region.

Complete mitochondrial genome sequence of the common bean anthracnose pathogen Colletotrichum lindemuthianum

Abstract Colletotrichum lindemuthianum is the causal agent of anthracnose in common bean (Phaseolus vulgaris), one of the most limiting factors for this crop in South and Central America. In this work, the mitochondrial sequence of a Colombian isolate of C. lindemuthianum obtained from a common bean plant (var. Cargamanto) with anthracnose symptoms is presented. The mtDNA codes for 13 proteins of the respiratory chain, 1 ribosomal protein, 2 homing endonucleases, 2 ribosomal RNAs and 28 tRNAs. This is the first report of a complete mtDNA genome sequence from C. lindemuthianum

The CD1/CD2 marker for specific detection of Colletotrichum lindemuthianum is an iron transporter pseudogene

Colletotrichum lindemuthianum, the causal agent of anthracnose in common bean (Phaseolus vulgaris), is one of the most yield-limiting factors worldwide. Anthracnose affects the quality of pods by inducing black, sunken cankers and can also affect petioles, leaf veins and stems where it induces the typical anthracnose sunken lesions. A few years ago, a duplex PCR method that combines amplification of an ITS rDNA segment (CY1/CY2) together with an uncharacterized RAPD-derived amplicon (CD1/CD2) was developed for specific detection of C. lindemuthianum. This study shows that the CD1/CD2 marker corresponds to a portion of an iron permease (Ftr1) pseudogene in the vicinity of the gene encoding for a polyhydroxyproline-rich protein in Colletotrichum. Discrimination with Colletotrichum orbiculare is due to a 15 nt deletion in the CY1 annealing region. The potential of using this genomic region for phylogenetic analysis of the C. orbiculare species complex and detection of their related species is discussed.

Characterization of the genome of a novel ilarvirus naturally infecting Cape gooseberry (Physalis peruviana)

As part of an initiative to characterize viruses infecting Cape gooseberry in the province of Antioquia (Colombia), we report the genome sequence of a new member of the genus Ilarvirus (family Bromoviridae). This virus was identified in a Cape gooseberry plot in the municipality of Marinilla in a mixed infection with potato virus Y (PVY) as part of high-throughput sequencing initiative. Results were confirmed by nested RT-PCR and DAS-ELISA. Phylogenetic analysis suggested that the Cape gooseberry ilarvirus is a new member of subgroup 1 and it is most closely related to ageratum latent virus (AgLV). The name “Cape gooseberry ilarvirus 1” (CGIV-1) is proposed for this new ilarvirus.

Genome comparison and primer design for detection of Tamarillo leaf malformation virus (TaLMV)

Abstract Tamarillo (Solanum betaceum Bosh) is a plant from the highland tropics of great importance in the fruit agroindustry of Colombia. In recent years, there has been a dramatic decrease in the local tamarillo fruit production as a result of an emerging disease caused by the potyvirus Tamarillo leaf malformation virus (TaLMV). Symptoms of TaLMV infection include rugose mosaics, severe leaf deformation, defoliation and reduction in plant longevity. In this work, we present a second genome sequence of TaLMV obtained from a tamarillo-growing region in northern Antioquia (Colombia). This genome was compared with a previously sequenced isolate from La Union in eastern Antioquia; this information was used to design specific primers targeting the CP and CI regions of the TaLMV. These primer sets will be useful in future epidemiological studies, seed certification schemes and genetic improvement programmes using real-time RT-PCR (RT-qPCR) and/or RT-PCR.